5HVK: LIMK1 mutant D460N

Crystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1. Determined by X-ray diffraction at 3.5 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,446
Mol. weight: 110.95 kDa
Ligands: MG, ANP
Released: 4 May 2016

Explore 5HVK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HVK contains 44 α-helices and 43 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	332-334	3	1
β-strand	339-344	6	1
β-strand	351-358	8	1
β-strand	364-370	7	1
α-helix	378-388	11
β-strand	396	1	2
α-helix	397-398	2
β-strand	399-403	5	1
β-strand	410-414	5	1
β-strand	420	1	2
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	3
α-helix	463-465	3
β-strand	466-468	3	2
β-strand	474-476	3	2
β-strand	483-484	2	3
β-strand	505	1	4
α-helix	518-521	4
β-strand	526	1	4
α-helix	529-544	16
α-helix	563-565	3
α-helix	566-570	5
α-helix	575-576	2
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-612	16
α-helix	619-630	12

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	5
α-helix	8	1
α-helix	9-18	10
α-helix	25-31	7
β-strand	33-40	8	5
β-strand	46-56	11	5
α-helix	67-74	8
β-strand	81-90	10	5
β-strand	96-104	9	5
α-helix	111-127	17
β-strand	134-137	4	5
α-helix	140-143	4
α-helix	147-153	7
β-strand	160-161	2	5
β-strand	164-165	2	5

Chain C: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	332-334	3	6
β-strand	339-344	6	6
β-strand	351-358	8	6
β-strand	364-370	7	6
α-helix	375-388	14
β-strand	396	1	7
α-helix	397-398	2
β-strand	399-403	5	6
β-strand	410-414	5	6
β-strand	420	1	7
α-helix	421-426	6
α-helix	434-453	20
β-strand	456-457	2	8
α-helix	463-465	3
β-strand	466-468	3	7
β-strand	474-476	3	7
β-strand	483-484	2	8
β-strand	505	1	9
α-helix	518-521	4
β-strand	526	1	9
α-helix	529-544	16
α-helix	563-565	3
α-helix	566-570	5
α-helix	575-576	2
α-helix	579-586	8
α-helix	591-593	3
α-helix	595-596	2
α-helix	597-612	16
α-helix	619-631	13

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	10
α-helix	9-18	10
α-helix	26-30	5
β-strand	33-40	8	10
β-strand	46-56	11	10
α-helix	57-59	3
α-helix	67-74	8
β-strand	81-91	11	10
β-strand	94-104	11	10
α-helix	111-125	15
β-strand	134-137	4	10
α-helix	140-143	4
α-helix	147-153	7
β-strand	160-161	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain kinase 1	A, C	protein	315	Homo sapiens	P53667 (AlphaFold model)
Cofilin-1	B	protein	165	Homo sapiens	P23528 (AlphaFold model)
Cofilin-1	D	protein	165	Homo sapiens	P23528 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5HVK_1 LIM domain kinase 1 (chains A, C)
GAMGSRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLK
EVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKD
IASGMAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDR
KKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNV
RGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQ
LDRGFWETYRRGESG

Sequence of entity 2 (B), FASTA

>5HVK_2 Cofilin-1 (chains B)
ASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVG
QTVDDPYTTFVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSK
DAIKKKLTGIKHELQANCYEEVKDRCTLAEKLGGSAVISLEGKPL

Sequence of entity 3 (D), FASTA

>5HVK_3 Cofilin-1 (chains D)
ASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDVG
QTVDDPYTTFVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSK
DAIKKKLTGIKHELQANCYEEVKDRCTLAEKLGGSAVISLEGKPL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. Hamill, S., Lou, H.J., Turk, B.E. et al. Mol Cell (2016) 62:397-408. DOI 10.1016/j.molcel.2016.04.001 · PubMed

Other PDB entries of the same protein (UniProt P53667 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3S95 1.65 Å, Crystal structure of the human LIMK1 kinase domain in complex with staurosporine
8AAU 1.74 Å, LIM Domain Kinase 1 (LIMK1) bound to LIMKi3
6WLY 1.9 Å, PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide
9Z6D 1.94 Å, Crystal structure of LIMK1 mutant D460N bound to small molecule inhibitor cLIMK1i
5HVJ 2.2 Å, Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP
5NXC 2.25 Å, LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736
9Z6E 2.26 Å, Crystal structure of apo LIMK1 mutant D460N
5L6W 2.53 Å, Structure Of the LIMK1-ATPgammaS-CFL1 Complex
7ATS 2.8 Å, The LIMK1 Kinase Domain Bound To LIJTF500127
7ATU 2.8 Å, The LIMK1 Kinase Domain Bound To LIJTF500025
7B8W 2.8 Å, Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470

Browse structure collections

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